3D Viewer help - "stretched" stacked images

[JoeG]

Hi all,

First time mailing list poster and relatively new user of ImageJ/Fiji here.

I am trying to use the 3D Viewer feature on stacked (.stk) files of yeast cells. When I do this it "separates" each slice as shown in the attached file. I cropped this image for simplification, but have the same result on all files. I have tried 3D Viewer with the sample images native to ImageJ/Fiji and have no problem, so I'm pretty sure the issue is with my files. I have also tried to "prep" the images in several ways by separating the stacked files, saving as .tiff or RGB, processing back to stacks/hyperstacks and always have the same results. Trying different numbers in the translation feature does not seem to make a difference.

All my drivers and updates are current.

Any advice is much appreciated.

Best,
Joe

[ctrueden]

Hi Joe,

> it "separates" each slice as shown in the attached file.

Try adjusting the "Voxel depth" in the Image Properties (shift+P after
opening your image). The 3D Viewer uses this information to decide how far
apart to space the slices.

Regards,
Curtis


On Sat, Feb 21, 2015 at 1:51 PM, JoeG <[hidden email]>
wrote:

> Hi all,
>
> First time mailing list poster and relatively new user of ImageJ/Fiji here.
>
> I am trying to use the 3D Viewer feature on stacked (.stk) files of yeast
> cells. When I do this it "separates" each slice as shown in the attached
> file. I cropped this image for simplification, but have the same result on
> all files. I have tried 3D Viewer with the sample images native to
> ImageJ/Fiji and have no problem, so I'm pretty sure the issue is with my
> files. I have also tried to "prep" the images in several ways by separating
> the stacked files, saving as .tiff or RGB, processing back to
> stacks/hyperstacks and always have the same results. Trying different
> numbers in the translation feature does not seem to make a difference.
>
> All my drivers and updates are current.
>
> Any advice is much appreciated.
>
> Best,
> Joe
> <http://imagej.1557.x6.nabble.com/file/n5011714/ImageJ_help.jpg>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/3D-Viewer-help-stretched-stacked-images-tp5011714.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[JoeG]

Hi Curtis,

Thanks for the reply, unfortunately this does not seem to make a difference. Any other thoughts?

Best,
Joe